Biomodeling: Introduction

• By using conda, one can make his own environment conveniently.

• Install miniconda https://docs.conda.io/en/main/miniconda.html

mkdir -p ~/miniconda3

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh

bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3

rm -rf ~/miniconda3/miniconda.sh 

~/miniconda3/bin/conda init bash

• Install Gromacs package using conda 

conda create -n gromacs

conda activate gromacs

conda install -c conda-forge gromacs=2023.1=nompi_cuda_ha81c2ac_2

• • Conda install command above tries to install Gromacs 2023.1 linked with CUDA library, assuming that you have an NVIDIA GPU.

  • Depending on the environment, you might need to choose another Gromacs image.

    • See https://anaconda.org/conda-forge/gromacs/files for available Gromacs images.

  • 
    

• After installation, “conda activate gromacs” will bring you to the installed environment.

• https://manual.gromacs.org/current/index.html

• If you have a Nvidia GPU, install CUDA toolkit before installing Gromacs

  • https://developer.nvidia.com/cuda-toolkit

cmake ../ \

-DGMX_BUILD_OWN_FFTW=ON \ 

-DGMX_DEFAULT_SUFFIX=OFF \ 

-DCMAKE_INSTALL_PREFIX=PATH_TO_GROMACS_INSTALLATION \ 

-DGMX_X11=OFF \

-DGMX_GPU=CUDA \

-DGMX_OPENMP=on \ 

-DGMX_PREFER_STATIC_LIBS=ON \

-DGMXAPI=OFF \

-DGMX_HWLOC=off

make

make install

source YOUR_INSTALLATION_DIRECTORY/bin/GMXRC.bash

Setup Gromacs environments:

• If you installed Gromacs using conda, 

  • conda activate YOUR_GROMACS_ENVIRONMENT

• If you compiled Gromacs package, you can set up environments by sourcing GMXRC.bash file

  • source PATH_TO_GROMACS_INSTALLATION/bin/GMXRC.bash

• 
  

Confirm Gromacs environments:

• Check if environmental variables such as $PATH, $GMXDATA etc are set up.

  • env

  • echo $GMXDATA

• Where is the Gromacs binary located?

  • which gmx

• See Gromacs manual pages

  • man gmx

  • man gmx mdrun

  • man gmx grompp

•  You need a text editor such as VIM, VS code, or something else.